ABSTRACT
Rapid whole genome sequencing of SARS-CoV-2 has presented the ability to detect new emerging variants of concern in near real time. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote "escape" from neutralizing antibodies in vitro. We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. Beginning in February 2021, only a small number (n=60) of isolates with this profile have been detected in the US, and only a total of 253 have been reported globally (first in the UK in December 2020). Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. Increased genomic surveillance will be crucial for detection of emerging variants of concern that can escape natural and vaccine induced immunity.
ABSTRACT
RT-qPCR is used world-wide to test and trace the spread of SARS-CoV-2. Extraction-less or direct RT-PCR is an open-access qualitative method for SARS-CoV-2 detection from nasopharyngeal (NP) or oral pharyngeal (OP) samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged ten global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international inter-laboratory ring trial. Participating labs were provided a common protocol, common reagents, aliquots of identical pooled clinical samples and purified nucleic acids, and used their existing in-house equipment. We observed 100% concordance across labs in the correct identification of all positive and negative samples, with highly similar Ct values observed. The test also performed well when applied to locally collected patient NP samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that open access, direct RT-PCR assays are a feasible option for more efficient COVID-19 testing as demanded by the continuing pandemic.
Subject(s)
COVID-19ABSTRACT
COVID-19 control efforts have been hampered by transmission from pre-symptomatic individuals infected with SARS-CoV2. Prolonged asymptomatic respiratory viral shedding in children has been described and may be another important reservoir for ongoing transmission. The primary diagnostic approach to identify SARS-CoV2 infection relies on qPCR of specific viral sequences from respiratory samples, which is expensive, uncomfortable, relatively slow, and susceptible to false-negative results. A rapid non-invasive method to detect mild or asymptomatic infection would have a major impact on public health campaigns to control COVID-19. We hypothesize that candidate biomarkers characterize the exhaled breath of children with SARS-CoV2 infection. To test this hypothesis, we enrolled SARS-CoV-2-infected and -uninfected children admitted to a major pediatric academic medical center and analyzed their breath volatile composition. Targeted volatiles analysis revealed that six volatile organic compounds increased significantly in SARS-CoV-2-infected children. Three aldehydes (octanal, nonanal, and heptanal) drew special attention as candidate biomarkers, because viral infections have previously been shown to induce aldehyde production. Together, these biomarkers demonstrated 100% sensitivity and 66.6% specificity. Our work provides a solid framework upon which to build a future "breathalyzer" test for SARS-CoV-2 infection in children.
Subject(s)
COVID-19 , Composite Lymphoma , Severe Acute Respiratory SyndromeABSTRACT
SARS-CoV-2 antibody responses in children remain poorly characterized. Here, we show that pediatric patients with multisystem inflammatory syndrome in children (MIS-C) possess higher SARS-CoV-2 spike IgG titers compared to those with severe coronavirus disease 2019 (COVID-19), likely reflecting a longer time since onset of infection in MIS-C patients.